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All over the city, innocent people are being mysteriously abducted. 13 Kamen Riders make contract with monsters from the Mirror World in order to be granted a wish. But to be given the wish, they must kill all the other Riders. In the Mirror World, which is a parallel dimension opposite our own, which only the monsters and Riders exist. Enter Shinji Kido, an intern at the online news service ORE Journal, who discovers one of the Advent Card decks at an apartment where every reflective surface has been covered by newspaper. He is about to be killed by a powerful dragon named Dragredder when he is saved by Ren Akiyama. Ren seeks to win the Rider War at all costs, in order to save his fiance who is a coma. Ren works with a young woman named Yui Kanzaki, who seeks her missing brother: the master of the Rider War, Shiro Kanzaki. Shinji contracts with Dragredder and becomes Kamen Rider Ryuki. He only wants to protect innocent people from the threat of the Mirror World, and stop the senseless fighting between the Kamen Riders.

After Kamen Rider Scissors died, Kamen Rider Zolda came into the fold but Shinji thought it was Goro Yura but in reality, it was super-lawyer Shuichi Kitaoka. Other Riders came along as Gai, Oja and Raia. Shinji managed to make friends with Raia, who had psychic abilities and foresaw Ren's death. Unfortunately he did not foresee Gais death to Ohja, a psychotic killer who had a grudge with his former lawyer Zolda. Gai had taken Yui hostage and fought against Knight & Ryuki, but Ohja and Zolda's battle crossed over. Gai's Contract Beast Metalgelas was infuriated at its master's death at the hands of Kamen Rider Ohja and went after him only to fall victim to Ohja's contract card, becoming the second monster to Ohja's collection. Shinji fought Knight twice, and each time could not bring himself to make the final strike. Gai hard stolen Shinji's Dragreder Advent card and Raia helped him retrieve it. When Ohja performed his Final Vent against Ryuki, Raia pushed him out of the way and took the attack instead. He died shortly afterwards due to his wounds.

After forming Contracts with Metalgelas and Evildiver upon killing their masters, Ohja can combine them with Venosnaker to create Genocider. Kamen Rider Odin appeared proclaiming himself as the "Final, 13th Rider". He used the Time Vent, which turned back time and only Shinji felt it. Another homicidal killer Tiger came along, professor Hideyuki Kagawa experimented with the decks, creating Kamen Rider Alternate and Alternate Zero. However, before Yui could be killed by the Contracted Monsters of the three Riders, she somehow manages to control them into attacking their masters. Deciding to take matters into his own hands, Kagawa attempted to kill Yui himself. However, Tiger betrayed Kagawa, claiming that in order to be a true hero, one had to win the Rider War. Tiger kills Kagawa. While watching Zolda, Ohja and Knight participate in a three-way battle, Satoru poured kerosene all over Zoldas car, destroying their only way out of Mirror World before being defeated by Ohja yet again. He ends up dying due to his injuries and as he died, he wondered about how he could have been a hero and the next day the newspaper labels him a 'hero.'

Kamen Rider Imperer, a plucky rich kid who clung to Knight & Ryuki, was dissolved when Ohja broke his deck. Zolda eventually died due to a disease and his assistant Goro was killed by Ohja in the Zolda armor. Ohja was killed by a barrage of fire by police. When Yuri was 7, she fell out of the chair and died. Yui's mirror reflection offered to give her a new life, but explained to Shiro that this life would run out when Yui became twenty. Shiro dedicated his life to saving Yui and created the Advent decks. Shiro eventually declares Ren as the last Rider. All the other Riders had died, but it was Shinji's death that devastated Ren. Shinji's dying words urged Ren into bringing the war to an end. Shiro Kanzaki brought him to fight the remaining Rider, Odin. As Ren was about to lose, Shiro Kanzaki was tormented by his sister Yui Kanzaki's words, and self-destroyed Odin, thus making Ren the final Rider. The wish appeared, and Ren used it to save Eri's life as he had originally intended. He might have died. After Shiro restored time to its proper course after Yui's death, Ren and Shinji gained a new life with no memory of being Riders. Shiro and Yui Kanzaki died in 1989. They moved into the Mirror World, to live with their adult Mirror World reflections.